How has geography determined history in the case of the New World's natives?
You can argue that geography determined the history of the Native Americans by isolating them from Eurasia for thousands of years prior to the coming of the Europeans starting in 1492. This isolation left them technologically inferior and without immunity to Old World diseases.
For whatever reason, (Jared Diamond's Guns, Germs, and Steel makes a good case for this being geographical as well) Eurasia was the center of the creation of technology for much of human history. Since the Native Americans were cut off from that technology, they were at a huge disadvantage when the Europeans "discovered" the Americas. They also lacked large domesticated animals like horses (for war and farming) and cows (for farming).
In addition, the Native Americans lacked immunity to Old World diseases. This meant that, upon contact, they died in the millions from diseases like smallpox that the Europeans carried with them. This helped to doom the Native Americans' societies.
You can argue, then, that geographic isolation determined the history of Native Americans at least from 1492 on.